These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: My Little Pony Friendship Is Magic S 3 E 13 Magical Mystery Cure
Alicorn Twilight. The idea was controversial before the episode aired. Now that it has the general consensus seems to be split between it being a good thing, that it's too early to tell, or it's a sign of Jumping the Shark.
Opinion is divided over how well the episode pulled off the above; whether it felt rushed and filled with too many songs instead of explaining events, or if this was a good way of condensing the plot down into a single episode without sacrificing the story-telling.
Designated Hero: Some fans feel that this episode puts Twilight firmly into this category.
Fan Dumb: Some fans took the opportunity to flog a dead horse and flame Yamino (A fan who was Mis-blamed for "Derpy Gate", an incident where Derpy's appearances were heavily edited in an episode) over Derpy's cameos in the episode.
Fanfic Fuel: Becoming an alicorn Princess is now something that can be earned?!
The same applies to the countless number of Alicorn!Twilight fan fics and pictures that existed before this episode was announced.
Getting back to the original conflict, you would not believe the number of "Twilight-screws-up-a-spell" fanfictions that were made in the past two years. It was considered cliche before the actual show got a chance to use it.
It's Short, so It Sucks : The main complaint on the episode (after the initial kerfuffle about Alicorn Twilight) seems to be that it felt a little rushed and should have been a two-parter. Most importantly, it was never explained what Twilight's change would mean. A tweet from Meghan McCarthy states that there will be two more episodes which will turn this episode into a three-parter, so it is possible that viewers will get more on the reason(s) for Twilight's transformation.
It Was His Sled: Thanks to news websites, The Hub's episode event title, and Hasbro reminding everyone about the new toyline (they built a life-size statue to show off at the New York Toy Fair), the whole fandom knew about Twilight becoming an Alicorn Princess weeks in advance, not counting rampant rumors even before that.
Worse still: Twilight fixed her mistake. Star Swirl couldn't. Did he test this spell, and, if so, how many lives did he ruin by mistake?
Spoiled by the Format: You know there's going to be more coming when it looks like the problem's solved and everything's going to be all fine and dandy with a third of the episode left.
Squick: The way Pinkie's legs bend when she tries to applebuck a tree during the Cutie Mark song... ow.
Tainted by the Preview: An "audio only" version of one of the songs in the episode, A True True Friend, was leaked on Internet five days before the episode aired, with it not having mixed reactions from people at Equestria Daily, but also hinted that the "swapped Cutie Marks" plot would be rushed for the sake of having Twilight become an alicorn in the final minutes.
Tear Jerker: Celestia singing just how proud she is of how far Twilight Sparkle has come.
The Mane Character's roles get swapped? Wait, what do you mean that it doesn't happen to the main Mane Character? We barely get to see results before Twilight figures out how to solve the problem, since the third act is needed for Twilacorn. As noted above, some fans think this should have been a two-parter. However, it's been stated that this episode will be turned into turned into a three-part story at the start of the fourth season.
Some fans were a bit dismayed that Twilight flew into the camera at the very end because an episode about her learning how to use to her new wings would have been nice. However, this one may not be an issue since a season 4 (or Equestria Girls) clip from Hot Topic shows Twilight trying to fly and falling flat on her face. So we might still get an episode for this.
The show has thus far only given hints as to how exactly Cutie Marks work and how much they signify. This would have been the perfect opportunity to go into this subject but once again they don't, except by implication. Plus, there's also the fact that the dilemma was solved with the most obvious and direct solution possible instead of having to make them work for the solution.
Visual Effects of Awesome: Special attention has been paid to the lighting of this episode: there are several beautiful instances of shading, and some lens flares have been added. Add to this some dynamic camera movements (particularly the first shot, imitating the opening theme song),the epic shot of Rarity struggling to control a storm during The Cutie Mark Song, some particularly smooth animation, especially on Alicorn Twilight, and the gorgeous Celestial Plane, and "Magical Mystery Cure" is the best-looking episode by a long shot.